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LINC01619 long intergenic non-protein coding RNA 1619 [ Homo sapiens (human) ]

Gene ID: 256021, updated on 17-Sep-2024

Summary

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Official Symbol
LINC01619provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 1619provided by HGNC
Primary source
HGNC:HGNC:27409
See related
Ensembl:ENSG00000257242 AllianceGenome:HGNC:27409
Gene type
ncRNA
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
C12orf79
Expression
Biased expression in bone marrow (RPKM 7.3), lymph node (RPKM 0.9) and 6 other tissues See more
Orthologs
all
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Genomic context

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See LINC01619 in Genome Data Viewer
Location:
12q21.33
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (91984976..92142831, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (91962471..92120393, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (92378752..92536607, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2404 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:92296093-92297292 Neighboring gene uncharacterized LOC105369901 Neighboring gene MPRA-validated peak1883 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr12:92356292-92356496 Neighboring gene NANOG hESC enhancer GRCh37_chr12:92415340-92415873 Neighboring gene Sharpr-MPRA regulatory region 2068 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:92471461-92472660 Neighboring gene Sharpr-MPRA regulatory region 10753 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:92501486-92502024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6719 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6720 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6721 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6723 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6722 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:92538603-92539139 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6725 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6726 Neighboring gene BTG1 divergent transcript Neighboring gene ribosomal protein L21 pseudogene 106 Neighboring gene BTG anti-proliferation factor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6727 Neighboring gene long intergenic non-protein coding RNA 2391 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6728 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6729 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:92718856-92719356 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:92719357-92719857 Neighboring gene NANOG hESC enhancer GRCh37_chr12:92725117-92725618 Neighboring gene uncharacterized LOC105369902 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6730 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6731

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Long Noncoding RNA LINC01619 Regulates MicroRNA-27a/Forkhead Box Protein O1 and Endoplasmic Reticulum Stress-Mediated Podocyte Injury in Diabetic Nephropathy. Bai X, et al. Antioxid Redox Signal, 2018 Aug 1. PMID 29334763
  2. Biological insights from 108 schizophrenia-associated genetic loci. Schizophrenia Working Group of the Psychiatric Genomics Consortium. Nature, 2014 Jul 24. PMID 25056061, Free PMC Article
  3. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. study demonstrates that LINC01619 functions as a competing endogenous RNA and regulates miR-27a/FOXO1-mediated ER stress and podocyte injury in diabetic nephropathy
    Title: Long Noncoding RNA LINC01619 Regulates MicroRNA-27a/Forkhead Box Protein O1 and Endoplasmic Reticulum Stress-Mediated Podocyte Injury in Diabetic Nephropathy.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

General gene information

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Markers

Homology

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

RNA

  1. NR_046159.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) contains an alternate 5' exon and an additional internal exon, and uses an alternate splice site in another internal exon, compared to variant 1.
    Source sequence(s)
    BC029844, CA438667
    Related
    ENST00000551843.5

  2. NR_046160.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) contains an additional internal exon and uses an alternate splice site in another internal exon, compared to variant 1.
    Source sequence(s)
    BC029844, BC118985, CA438667, DB121637

  3. NR_132339.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript.
    Source sequence(s)
    AK055439, BC029844, CA438667, DB121637
    Related
    ENST00000549802.5

  4. NR_132340.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in an internal exon, compared to variant 1.
    Source sequence(s)
    BC029844, BC107595, CA438667, DB121637

  5. NR_132341.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses two alternate splice sites in an internal exon, compared to variant 1.
    Source sequence(s)
    BC029844, BC122534, CA438667, DB121637

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    91984976..92142831 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    91962471..92120393 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001256373.1: Suppressed sequence

    Description
    NM_001256373.1: This RefSeq was removed because currently there is support for the transcript but not for the protein.

  2. NM_001256374.1: Suppressed sequence

    Description
    NM_001256374.1: This RefSeq was removed because currently there is support for the transcript but not for the protein.

  3. NM_001256375.1: Suppressed sequence

    Description
    NM_001256375.1: This RefSeq was removed because currently there is support for the transcript but not for the protein.
Nucleotide Protein
Heading Accession and Version

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